[R] error in chol.default((value + t(value))/2) : , the leading minor of order 1 is not positive definite

Troels Ring tring @ending from gvdnet@dk
Sat May 5 10:19:48 CEST 2018


Dear friends - I'm having troubles with nlme fitting a simplified model 
as shown below eliciting the error

Error in chol.default((value + t(value))/2) :
   the leading minor of order 1 is not positive definite -

I have seen the threads on this error but it didn't help me solve the 
problem.

The model runs well in brms and identifies the used parameters even with 
fixed effects for TRT  - but here in nlme TRT is ignored and I guess 
this is not the reason for the said error

Below is the quite clumsy simulated data set and specification of call 
to nlme - the start values are taken from fitted values in brms

library(ggplot2)
windows(record=TRUE)
#generate 3*10  rats - add fixed effects to the four parameters 
according to the three groups - add random effects pr each rat - add 
residual random effect
#Parameter values taken from Sapirstein AJP 181:330-6, 1955


set.seed(1234)
Time <- seq(1,60,by=1)
A <- 275; B <-  140;  g1 <- 0.1105; g2 <- .0161

N <- 30

AA <- rep(A,30)+rnorm(30,0,30);BB <- rep(B,30)+rnorm(30,0,15) ;
gg1 <- rep(g1,30)+rnorm(30,0,0.01); gg2 <- rep(g2,30)+rnorm(30,0,0.001)

TRT <- gl(3,10*60)
levels(TRT) <- c("CTRL","DIAB","HYPER")
AA1 <- AA + c(rep(0,10),rep(10,10),rep(-10,10))
BB1 <- BB + c(rep(0,10),rep(5,10),rep(-5,10))
Gg1 <- gg1 + c(rep(0,10),rep(0.01,10),rep(-0.01,10))
Gg2 <- gg2 + c(rep(0,10),rep(0.005,10),rep(-0.005,10))

getY <- function(A,B,g1,g2) {
Y  <- A*exp(-g1*Time) + B*exp(-g2*Time)
Y <- Y + rnorm(60,0,20)
}
YY <-  c()
for (i in 1:N) YY <- c(YY,getY(AA1[i],BB1[i],Gg1[i],Gg2[i]))
TT <- rep(Time,N)
RAT <- gl(N,length(Time))
dats  <- data.frame(RAT,TRT,TT,YY)
Dats <- dats
names(Dats)[c(3,4)] <- c("Time","Y")
dput(Dats,"dats0505.dat")

with(Dats,plot(Time,Y,pch=19,cex=.1,col=TRT))
ggplot(data=Dats,aes(x=Time,y=Y,group=RAT,col=TRT)) + geom_line()

library(nlme)

gfr.nlme <- nlme(Y ~ A*exp(-Time*g1)+B*exp(-Time*g2),
data = Dats,
fixed = A+g1+B+g2 ~1,
random = A+g1+B+g2 ~1,groups = ~ RAT,
start = c(255,115,130*1e-3,17*1e-3),
na.action = na.omit,verbose=TRUE,control = list(msVerbose = TRUE))
summary(gfr.nlme)



More information about the R-help mailing list